An Avirulent Ralstonia Solanacearum Strain Undergoes Phenotype Conversion from a Pathogenic Strain Under Natural Environment

An avirulent R. solanacearum strain named FJAT-1458 was isolated from living tomato vessel and it showed no toxicity to tomato, pepper and eggplant. Multilocus sequence analysis (MLSA) based on eight genes (egl, hrpB, mutS, pehA, recA, rpoA, rpoB and rpoC) and whole genome average nucleotide identity (ANI) analysis suggested that strain FJAT-1458 belong to phylotype I. Genome sequence of the strain FJAT-1458 revealed a circular chromosome and a circular megaplasmid with whole genome size of 6,059,899 bp and GC content of 66.78%. Functional annotation of FJAT-1458 showed a total of 5,442 genes, with 5,166 protein-encoding genes, 202 pseudogenes and 74 noncoding RNA genes. Among which, 3,938 protein-coding genes can be assigned to 23 COG families, and 1,521 of them had KEGG orthologs. Prophage prediction using PHASTER revealed 12 prophages, including 7 intact, 1 questionable and 4 incomplete prophages. Comparative genome analyses between GMI1000 and FJAT-1458 showed that most of the virulence factors were well conserved and only small portion of them were distinct between them. Two genes, including a methyltransferase and an ISL3 family transposase genes, were identified to be inserted immediately upstream (141 bp) of phcA gene, which assumed to be responsible for avirulence of strain FJAT-1458. It is suggested that strain FJAT-1458 was originated from a wild-type pathogenic strain through an accident phenotype conversion, which is like those when cultured under experimental conditions. Our study provides new insight into the evolution of virulence in R. solanacearum strain under natural environment.